When running the pipeline with a single sample you get the following error when running the Salmon step.
Execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 0.
The full error message was:
Error executing process > 'alignment_free_quant:QuantMerge (Salmon QuantMerge pre_NFpipeline)'
Caused by:
Missing output file(s) *.txt expected by process alignment_free_quant:QuantMerge (Salmon QuantMerge pre_NFpipeline)
Command executed:
salmon quantmerge -c numreads --quants {Breast} -o pre_NFpipeline_transcripts_quantmerge_numReads.txt
salmon quantmerge -c tpm --quants {Breast} -o pre_NFpipeline_transcripts_quantmerge_TPM.txt
salmon quantmerge -c len --quants {Breast} -o pre_NFpipeline_transcripts_quantmerge_Length.txt
salmon quantmerge -c elen --quants {Breast} -o pre_NFpipeline_transcripts_quantmerge_EffectiveLength.txt
Command exit status:
0
Command output:
[2021-03-03 00:38:17.817] [mergeLog] [info] samples: [ {Breast} ]
[2021-03-03 00:38:17.817] [mergeLog] [info] sample names : [ {Breast} ]
[2021-03-03 00:38:17.817] [mergeLog] [info] output column : TPM
[2021-03-03 00:38:17.817] [mergeLog] [info] output file : pre_NFpipeline_transcripts_quantmerge_numReads.txt
[2021-03-03 00:38:17.817] [mergeLog] [critical] The sample directory {Breast} either doesn't exist, or doesn't contain a quant.sf file
[2021-03-03 00:38:17.864] [mergeLog] [info] samples: [ {Breast} ]
[2021-03-03 00:38:17.864] [mergeLog] [info] sample names : [ {Breast} ]
[2021-03-03 00:38:17.864] [mergeLog] [info] output column : TPM
[2021-03-03 00:38:17.864] [mergeLog] [info] output file : pre_NFpipeline_transcripts_quantmerge_TPM.txt
[2021-03-03 00:38:17.864] [mergeLog] [critical] The sample directory {Breast} either doesn't exist, or doesn't contain a quant.sf file
[2021-03-03 00:38:17.891] [mergeLog] [info] samples: [ {Breast} ]
[2021-03-03 00:38:17.891] [mergeLog] [info] sample names : [ {Breast} ]
[2021-03-03 00:38:17.891] [mergeLog] [info] output column : TPM
[2021-03-03 00:38:17.891] [mergeLog] [info] output file : pre_NFpipeline_transcripts_quantmerge_Length.txt
[2021-03-03 00:38:17.891] [mergeLog] [critical] The sample directory {Breast} either doesn't exist, or doesn't contain a quant.sf file
[2021-03-03 00:38:17.917] [mergeLog] [info] samples: [ {Breast} ]
[2021-03-03 00:38:17.917] [mergeLog] [info] sample names : [ {Breast} ]
[2021-03-03 00:38:17.917] [mergeLog] [info] output column : TPM
[2021-03-03 00:38:17.917] [mergeLog] [info] output file : pre_NFpipeline_transcripts_quantmerge_EffectiveLength.txt
[2021-03-03 00:38:17.917] [mergeLog] [critical] The sample directory {Breast} either doesn't exist, or doesn't contain a quant.sf file
The problem is that there are no outputs from the QuantMerge step in https://github.com/UMCUGenetics/RNASeq-NF/blob/master/sub-workflows/alignment_free_quant.nf
This step is not needed for a single sample because there is only 1 output to merge.
A solution would be to check how many samples are being analysed. If it is only 1 sample, skip the QuantMerge step and set the single quant.sf file as output.
When running the pipeline with a single sample you get the following error when running the Salmon step.
The problem is that there are no outputs from the QuantMerge step in https://github.com/UMCUGenetics/RNASeq-NF/blob/master/sub-workflows/alignment_free_quant.nf
This step is not needed for a single sample because there is only 1 output to merge.
A solution would be to check how many samples are being analysed. If it is only 1 sample, skip the QuantMerge step and set the single quant.sf file as output.